Biology subjects

Schoof, H.

Publications and source records attributed to Schoof, H..

9 recordsLinked to original sources

bioRxiv2026

In silico restriction site analysis of whole genome sequences shows patterns caused by selection and sequence duplications

Biological sequences are known to be not random. Thus, the comparison of in silico restriction fragment distributions of random and biological sequences may be an indicator of this non-randomness. Our analyses show that for most of the tested combinations of restriction enzyme and genome sequence the fragments per Megabase of the biological sequence deviate at least more then 10% from the corresponding random sequence. This deviation goes into both directions, i.e. clearly increased values are as common as clearly decreased values. Although there is no species- or restriction-enzyme-specific effect, a clear impact of the GC content both of the restriction site and of the genome sequence can be seen. In contrast to the random sequences, the genome sequences show distinct peaks in their fragment length distributions, hinting to repetitive elements such as transposons.

genomics↗

bioRxiv2025

Integration of differential expression under drought with gene family expansion unique to drought tolerant species predicts candidate genes for drought adaptation in Brassicaceae species.

BackgroundIn order to predict candidate genes for drought adaptation, we analyze genomic data of the more drought resistant Brassicaceae species Eutrema salsugineum and Arabidopsis lyrata compared to more drought sensitive species Arabidopsis thaliana and Brassica napus. We combine gene family expansion, which is an important driver of evolution in plants, unique to the drought resistant species with differential expression under drought (DE). ResultsWe show that combining trait-specific gene family expansion with differential expression predicts a concise set of candidate genes. To demonstrate that these are relevant for drought adaptation in tolerant species we show enrichment of DE conserved between both tolerant species, DE unique to the tolerant species, and up regulation. We show that specific functions are enriched, and that the set contains genes with functions such as root development in line with drought adaptation based on evidence from other species, while the background of all differentially expressed genes (DEGs) contains many general stress reaction genes. Whereas DEGs in general are rarely under diversifying selection, signatures of diversifying selection are slightly enriched in the candidate gene families, highly significantly enriched in DEGs in tolerant species-specific expanded gene families, and in contrast not enriched in DEGs in sensitive species-specific expanded gene families. ConclusionsOur approach identifies a concise and functionally relevant set of candidate genes for drought adaptation with promising targets for functional studies and crop improvement for drought tolerance. We propose that our method can also be used to predict candidate genes for adaptation to other environmental factors.

plant biology↗

bioRxiv2024

Regulation of heterosis-associated gene expression complementation in maize hybrids

The dominance model of heterosis explains the superiority of F1-hybrids via the complementation of unfavorable by beneficial alleles in many genes. Consistent with this model, genes active in only one parent and the hybrid display single-parent expression (SPE) complementation. Here we demonstrated, that SPE can explain up to 29% of heterotic variance in maize (Zea mays L.). Moreover, expression quantitative trait loci (eQTL) revealed, that the genotype of the active parent determines the regulation mode of SPE patterns in cis or trans, which might explain how phylogenetic distance translates to transcriptomic diversity and heterosis in hybrids. Furthermore, we showed that most eQTL are located in heterozygous regions of the genome and that a trans eQTL controls the activity of a SPE gene which regulates lateral root density in hybrids. We anticipate that our study will stimulate further research elucidating the regulation and molecular mechanisms underlying heterosis.

plant biology↗

bioRxiv2024

NUDIX Hydrolases Target Specific Inositol Pyrophosphates and Regulate Phosphate and Iron Homeostasis, and the Expression of Defense Genes in Arabidopsis

Inositol pyrophosphates (PP-InsPs) are important signaling molecules that regulate diverse cellular processes in eukaryotes, including energy homeostasis, phosphate (Pi) signaling, and phytohormone perception. Yet, in plants, the enzymes responsible for their turnover remain largely unknown. Using a non-hydrolysable PP-InsP analog in a pull-down approach, we identified a family of Arabidopsis NUDIX hydrolases (NUDTs) that group into two closely related subclades. Through in vitro assays, heterologous expression systems, and higher-order gene-edited mutants, we explored the substrate specificities and physiological roles of these hydrolases. Using a combination of strong anion exchange (SAX)-HPLC, PAGE, and capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS), we found that their PP-InsP pyrophosphatase activity is enantiomer-selective and Mg2+-dependent. Specifically, subclade I NUDTs preferentially hydrolyze 4-InsP7, while subclade II NUDTs target 3-InsP7, with minor activity against other PP-InsPs, including 5-InsP7. In higher-order mutants of subclade II NUDTs, we observed defects in both Pi and iron homeostasis, accompanied by increased levels of 1/3-InsP7 and 5-InsP7, with a markedly larger increase in 1/3-InsP7. Ectopic expression of NUDTs from both subclades induced local Pi starvation responses (PSRs), while RNA-seq analysis comparing wildtype (WT) and subclade II nudt12/13/16 loss-of-function plants indicates additional PSR-independent roles, potentially involving 1/3-InsP7 in the regulation of plant defense. Consistently, nudt12/13/16 mutants displayed enhanced resistance to Pseudomonas syringae infection, indicating a role in bacterial pathogen susceptibility. Expanding beyond subclade II NUDTs, we demonstrated susceptibility of the 3PP-position of PP-InsPs to enzymatic activities unrelated to NUDTs, and found that such activities are conserved across plants and humans. Additionally, we found that NUDT effectors from pathogenic ascomycete fungi exhibit a substrate specificity similar to subclade I NUDTs. Collectively, our findings reveal new roles for NUDTs in PP-InsP signaling, plant nutrient and immune responses, and highlight a cross-kingdom conservation of PP-InsP-metabolizing enzymes.

plant biology↗

bioRxiv2024

Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm

The BonnMu resource is a transposon-tagged mutant collection designed for functional genomics studies in maize. To expand this resource, we crossed an active Mutator (Mu) line with dent (B73, Co125) and flint (DK105, EP1 and F7) germplasm, resulting in the generation of 8,064 mutagenized BonnMu F2-families. Sequencing of these Mu-tagged families revealed 425,924 heritable Mu insertions affecting 36,612 (83%) of the 44,303 high-confidence gene models of maize (B73v5). On average, we observed 12 Mu insertions per gene (425,924 total insertions/ 36,612 affected genes) and 53 insertions per BonnMu F2-family (425,924 total insertions/ 8,064 families). Mu insertions and photos of seedling phenotypes from segregating BonnMu F2-families can be accessed through the Maize Genetics and Genomics Database (MaizeGDB). Downstream examination via the automated Mutant-seq Workflow Utility (MuWU) identified 94% of the germinal insertion sites in genic regions and only a small fraction of 6% inserting in non-coding intergenic sequences of the genome. Consistently, Mu insertions aligned with gene-dense chromosomal arms. In total, 42% of all BonnMu insertions were located in the 5 untranslated region (UTR) of genes, corresponding to accessible chromatin. Furthermore, for 38% of the insertions (163,843 of 425,924 total insertions) Mu1, Mu8 and MuDR were confirmed to be the causal Mu elements. Our publicly accessible European BonnMu resource has archived insertions covering two major germplasm groups, thus facilitating both forward and reverse genetics studies.

genomics↗

bioRxiv2022

Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity

The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. This might lead to a cascade of suspended sink-source activities, which ultimately delay organ development and differentiation in barley shoot meristems under short photoperiods.

developmental biology↗

bioRxiv2021

ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIVE containing protein that controls root growth angle in barley and wheat

The root growth angle defines how roots grow towards the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience and as a consequence yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin independent higher responsiveness to gravity compared to wild type plants. We cloned the EGT2 gene by a combination of bulked segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. Subcellular localization experiments revealed that EGT2 localizes to the nucleus and cytoplasm. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA-seq, we observed that seven expansin genes were transcriptionally downregulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals. Significance StatementTo date the potential of utilizing root traits in plant breeding remains largely untapped. In this study we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain containing protein. We demonstrated that EGT2 is a key gene of root growth angle regulation in response to gravity which is conserved in barley and wheat and could be a promising target for crop improvement in cereals.

plant biology↗

bioRxiv2019

Global transcriptome profiling uncovers footprints of root and shoot development in crop models barley and tomato

Land plants establish their forms at two development hotspots- root and shoots apices. In this study, we dissected and compared the global transcriptome of these developmental zones in crop models barley and tomato. We employed a state of the art transcriptome analysis technique for deep profiling of expressed genes. This analysis resulted in highly reproducible quantitative expression profiles of 19,441 and 23,388 genes in barley and tomato, respectively. In barley, 16,834 genes were expressed both in root and shoot apices, whereas 1,081 genes were specific to root apex and 1,526 genes were active in shoot apex. With significant variations 20,154 genes were expressed in root and shoot apices of tomato of which 1,858 and 1,376 genes showed root and shoot specificities. Systematic analyses of these genes revealed distinct commonalties and divergence among the active genes for root and shoot development. A deeper insight in these data uncover tissue- and species specific genes, unique footprints of gene ontologies and divergence of auxins pathway genes in root and shoot apices of barley and tomato. These data provide a primary resource to understand intra- and inter-species genetic networks of root and shoot development as well as the evolution of genes in crop plants.

genomics↗

bioRxiv2019

A systemic approach provides insights into the salt stress adaptation mechanisms of contrasting bread wheat genotypes

Bread wheat is one of the most important crops for human diet but the increasing soil salinization is causing yield reductions worldwide. Physiological, genetic, transcriptomics and bioinformatics analyses were integrated to study the salt stress adaptation response in bread wheat. A comparative analysis to uncover the dynamic transcriptomic response of contrasting genotypes from two wheat populations was performed at both osmotic and ionic phases in time points defined by physiologic measurements. The differential stress effect on the expression of photosynthesis, calcium binding and oxidative stress response genes in the contrasting genotypes supported the greater photosynthesis inhibition observed in the susceptible genotype at the osmotic phase. At the ionic phase genes involved in metal ion binding and transporter activity were up-regulated and down-regulated in the tolerant and susceptible genotypes, respectively. The stress effect on mechanisms related with protein synthesis and breakdown was identified at both stress phases. Based on the linkage disequilibrium blocks it was possible to select salt-responsive genes as potential components operating in the salt stress response pathways leading to salt stress resilience specific traits. Therefore, the implementation of a systemic approach provided insights into the adaptation response mechanisms of contrasting bread wheat genotypes at both salt stress phases.\n\nHighlightThe implementation of a systemic approach provided insights into salt stress adaptation response mechanisms of contrasting bread wheat genotypes from two mapping populations at both osmotic and ionic phases.

systems biology↗